And the number of new cholera infections has more than doubled over the past fortnight.
Ministry of Health spokesman Quinhas Fernandes said "4,518 cases of cholera and 41 deaths have been recorded since December 25, 2014".
Authorities said the hardest hit region is the coal-rich western Tete province, which borders Zimbabwe and Malawi.
Although Tete was not affected by recent floods, its capital city alone has recorded more than 1,500 cases over the past two months, and the pace of infections is quickening there, while elsewhere it is stabilising.
This year, heavy rains and floods that hit the country between December and January killed 158 people and affected 170,000, hastening the spread of cholera.
Mozambique's deadliest floods were in 2000, when an estimated 800 people were killed.